I find the Sony library good for reading ebooks on the screen (I like the option of reading fullscreen,2 pages at a time, something Adobe doesn't even offer on their PDF readers!)
And then there is that it's currently my only program installed that reads LRF files on my comp.

This has been suggested to Kovid and he is not against the idea but says he has other things he would rather add first. He does accept patches so you are welcome to add a "don't reorganize my library" type option to the software I'm sure he would integrate it.
BOb

I'm very picky about my library, and while I tried using Calibre's GUI/Database it just doesn't work for me. As a workaround, you can bypass using Calibre's GUI and instead use Prs505 File Manager. This allows you to continue to use Calibre's essential console utilities while bypassing the unwanted library reorganization. The program is a little rough around the edges, but I'm finding it to be quite usable. But yes, a Calibre "do not reorg my library" switch would be preferable.

I'm very picky about my library, and while I tried using Calibre's GUI/Database it just doesn't work for me. As a workaround, you can bypass using Calibre's GUI and instead use Prs505 File Manager. This allows you to continue to use Calibre's essential console utilities while bypassing the unwanted library reorganization. The program is a little rough around the edges, but I'm finding it to be quite usable. But yes, a Calibre "do not reorg my library" switch would be preferable.

So you don't use the PRS 505 GUI? Because if you did it is still storing your ebooks in a database. The difference with calibre is that the "database" also consists of the file system. In both versions calibre was storing a copy of your book somewhere. However, as has been said about, it doesn't touch your current book or move it, or delete it.

BTW: You can install calibre and only use the command line utilities also.

Problem here is that you have to select one directory for both the IN and OUT,meaning the organized and non organized library (choose which one of the two is organized according to you).

Meaning that in my organized library, Calibre will start reading, and copying the files to that same directory.
It's not like I can say:"Organize them to/on my SD card",or so...

Yes, you can. You open the Configuration button on the right of the search field past the reset, and you set the location. This would be your 'OUT' and the internal library for calibre. Your 'IN' can be from selected from anywhere when Importing titles. I have a books directory with a rather intricate hierarchy myself, only about a quarter of which are destined for the Sony Reader. So I keep a seperate spot for calibre's database and books which I store on a USB HD.

I have a large library on my pc of pdf books of all sorts of styles, and writers.
And it seems like one program has managed to completely mess up the directory structure of my library!

Right now hundreds of directories have been created with names of authors, and all kinds of crap, which literally pisses me off, and I can only think of 2 programs that could be responsible for this mess!

1- Calibre
2- Sony reader Library...

Man, I'm surely PISSED OFF! Now hundreds of pdf's are not in the folders they where supposed to be!
I never agreed on rearranging (or messing up) my library!

And I want to know which of the 2 is responsible!

If it would be Calibre, I would very strongly urge to remove the auto arrangements, as it has brought me in a mess which will cost me several several and several hours of more work to place everything back again!!!!!

Needless to say the program responsible for the mess will immediately be removed from my computer!

I was so hesitant to install anything on my pc, even the Sony Library;since I don't like modifications to my already wonderful and speedy working OS.
It seems my cautiousness was not enough to protect me from an even greater disaster!

I will probably spend several days re-organising my library once again,that is, if I still will find in which folders all documents originally belonged.

Consider this as a serious complaint against one of the 2 programs!
I have no problem any program accessing my collection,however modifying it without prior notice is not an option!

*Edit: I found out (to my great displeasure), it is Calibre who re-organized my library. Pitty,because I did use the feeds the program offered! As soon as Calibre offers an update that will allow the user to make clear that it can not modify any books or the structure of the library, I might reconsider re-installing the program again.*